Captain Muto
by blackhole freedom
Summary: After Yugi loses the final duel against Atem, he runs away claiming he wants to get stronger and isn't seen for years. When his friends find him at last, it is in the most unlikely of places and under less than great circumstances. Will they be able to save him or will Army Captain Yugi Muto die as a high priority captive of enemy soldiers? Slightly OOC, but you'll see why soon.
1. Leaving

Hello, readers. This is my first story, so please read and let me know how I'm doing. I accept construtive critisism, but any flames will go in my fireplace where they belong! There will be very little romance in this story, just friendship and family. That does not mean there won't be any action. I intend for plenty of action. Without futher adoo, I give you "Captain Muto."

* * *

17 year old Yugi fell to his knees, utterly miserable with guilt. He had lost. He had lost and now Atem was trapped in this world for who knew how long. They were all so sure that he would win after he defeated the Egyptian God Cards, but it hadn't been enough. He wasn't sure how long he sat there, in the ancient tomb, but he was eventually led out when the tomb started to collapse. He didn't realize until afterwards when he and his friends were safe in warm sand of Egypt, that it was Atem who got him out. He looked up at the person who he looked up to an older brother and nearly broke down.

"I'm sorry! I'm so sorry!" Yugi exclaimed.

"Don't worry. It wasn't your fault," Atem tried desperately to comfort his younger brother, because that's what Yugi was to him, a brother.

"How am I not supposed to worry? You're trapped again! What's going to happen now?"

"I don't know, but we'll figure something out. Everything is going to be fine. You can't get too upset alright."

"Alright, I'll try," Yugi said, trying to smile but failing miserably.

* * *

When they returned to Domino City, Grandpa Muto welcomed Atem to live at the Game Shop giving him the guest bedroom, and saying they could get it more customized decorations in a few days. He was trying very hard to keep Atem's mind off his current situation. Yugi was very quiet, speaking only when someone asked a direct question, and answering shortly. When they were on their way to bed, Atem stopped Yugi at the top of the stairs.

"Yugi. I have something for you." Atem had an almost mischievous smile, which confused Yugi.

"What?"

"I have something for you," Atem said pulling something out of his pocket. "You earned these today. Despite what you may think, you are strong." Then he handed Yugi the Egyptian God Cards.

"Not strong enough. Atem I can't take these." He tried to give them back, but Atem wouldn't take them.

"Yes you can, and you will. You defeated them in battle. That means they are rightfully yours. You are still the King of Games. You just need to realize it."

"No, I'm not. I'm still weak," Yugi sighed.

Yugi went to his room without another word, taking the three Duel Monsters cards with him. Atem thought about going after him, but decided Yugi needed to be alone and might want to talk in the morning. If he knew that was the last time he would see his brother for several years, he would have made a different decision. When Yugi got to his room, he began to pack his duffel bag with clothes, money, his ID and lastly, reluctantly, the Egyptian God Cards. He wrote a letter and left it on his desk, before climbing out his second story window, not to see his family again for nearly six years.

When Atem went to wake his little brother up, he was shocked to find the bed empty and not slept in. He was horrified when he read the letter on the desk.

_I can't stay here. I'm sorry, but I have to become stronger. I'm not sure how, but when I do, I'll come back. Too many people I care about have been hurt because of me. When I am stronger, I'll be able to help Atem and keep the rest of my friends and family safe._

_ Yugi Muto_


	2. Five Years Later

Hello all. First I am sorry that I took so long but, college must come first. Second I want to thank Konoha's Hanyou Kunoichi, Doragon-chan, and DaisetsuChan for your wonderful reviews. They're what convinced me to get off my but and continue writing. Sorry that the last chapter was short. I just wanted to set the stage and show Yugi's original personality. Also after the first chapter, the story will be set about five years in the future and what happened in between will be shown as flash backs. Tell me if you think it works. Oh, and I'll try to make them longer too!

* * *

Five Years Later

Atem Muto woke up in his ever-familiar egyptian-inspired room at the Kame Game Shop still feeling exhausted, even though he had gotten a full nights sleep. He had returned the evening before from yet another trip to look for his brother Yugi, this time in Greece. And like every other excursion, all of his leads turned into dead ends. He dreaded getting ready and meeting up with his friends today, but knew putting it off wouldn't help. With a frustrated sigh, he pushed off his tan covers and went downstairs to the kitchen where his 'Grandpa' was making breakfast.

While he was not related to his family by blood, and technically was thousands of years older than them, they acted and felt as if they were and everyone outside their close circle of friends believed that the former ruler of Egypt was truly just Atem Muto, small time duelist, eldest grandson of Solomon Muto and brother to the famed Yugi Muto. In the years since their separation Atem, while still obsessed with finding his younger brother, had made a decent life for himself in Domino City. The year before, he had graduated from Domino Community College with and business degree and was now running the new Game Shop on the other side of town that he had helped his grandfather open with the previously mentioned business degree. He and Tea had dated for a few months three years before but decided to break it off and were now close friends. One thing that had been a surprise was that his new body was ageing normally and he was now five foot six inches tall and looked twenty-four; it seemed like he wouldn't be trapped here after all. He could live a normal life and then move on. Atem often asked himself that if Yugi knew this, would he come home, but never came up with a strait answer.

Pushing his thoughts aside for the moment, Atem said "Goodmorning" to Grandpa and sat down at the table, where a steaming plate of eggs, bacon and toast was waiting for him.

"Goodmorning. Did you sleep well, you don't look to good," Grandpa said, with a small smile, looking every bit the concerned grandfather that he was.

"Yes, I'm fine. Just worried is all. I couldn't find one useful thing in Greece. I'm running out of ideas," Atem said with a frustrated sigh.

Grandpa sat down across from Atem, looked into his adoptive grandsons eye, and sighed. "You know as well as I do that Yugi will only be found when he wants to be."

"But, what if something has happened to him? What if he were in trouble and couldn't reach anyone?"

"You will just have to trust that he can handle himself in whatever situation he might get into... Do you know that today is the aniversary? It's all over the news. Four calls have already come in asking for an interview or come kind of comment. It's rediculous!" Grandpa huffed.

Atem chuckled at this. "It is kind of funny. He was already famous when he was here, but after he disappeared that fame skyrocketed. People think he is more mysterious now."

"Well, they should mind their own buisness," he said as his grandson smiled in agreement.

After finishing breakfast, Atem went back up stairs to shower and change into blue pants and a white, button-up shirt with a black jacket on top. He then hurried out the front door to meet his friends, say goodbye to Grandpa as he went.

* * *

When Atem reached his and his friends normal meeting place, a burger joint a few blocks from Kaiba Corp, he was not surprised to see everyone else already there waiting for him. They were in a half-circle booth, from left to right sat Joey, Serenity, Tea, Tristan, and surprising as it may seem Mokuba and Seto who had joined their close-knit group after Egypt when he finally admitted that what they had been telling them was true. Atem walked over to the table sitting down next to Joey and exchanging hellos with everyone. After a few minutes of comfortable silence, Mokuba spoke up.

"So did you find anything?" he seemed apprehensive, like he didn't want to hear the answer, but knew someone had to ask.

"No, I didn't," Atem looked down sadly and stared at the table.

"It's okay, I'm sure we'll figure something out soon."

"I don't really want to talk about it. Tell me about what happened here while I was gone."

"Well," Tea spoke up, "The dance studio is going well. My students are progressing faster than I expected them to."

"Yeah, and I won a duel monsters tournament. It would have been great if you were there!" Joey said, his voice full of enthusiasm.

"I've just been studying," said Serenity.

"Yeah, you know, just doin' odd jobs and stuff. Same old, same old," said Tristan.

"That all sounds great," said Atem, "What have you been doing Seto. You've been awfully quiet this whole time."

"Work," said Seto. Atem frowned at the unusually short answer.

Mokuba started laughing quietly at this. "Don't worry. Biig brother is just brooding about a conference the board of directors is making him go to."

"Please, don't remind me," said Seto, earning poorly concealed laughter from the rest of the table.

"A conference? Where is it... and what is it for?"

* * *

Meanwhile...

Another young man was making his rounds in a military camp in the middle of the desert, making sure all his subordinates were doing their jobs. He beared a striking resemblance to Atem, from his hieght to his violet eyes which had lost the child-like gleam they once held. There were some differences though. He was slightly tanned and though not overly muscled, could definately be seen as lean under his standard issue desert fatigues. The biggest difference was his hair. Instead of the wild star shape it used to be, it was now cut close to his head and mostly black with a small bit of blond at the front that if allowed to grow out would become bangs.

As Yugi walked from station to station, he let his mind wander and began thinking of how his life had become what it was now. He had been traveling around for about a month and was almost out of money. He wasn't sure what he was going to do, but knew he could not return to Domino City yet. That was when he walked by the Army Recruting Center. It was a long shot, but it might be what he was looking for. He took a chance and went in. The recruter thought it was a joke at first, but let him sign up for the reserves. Basic Training had been horrible, but when it was over he was a different person, more refined and diceplined, and began to shoot through the ranks because of his strategiing skills. When he turned 18, he became a member of the regular military and was deployed to Iran. His current deployment was his fourth, each time he had made more accomplishments and climbed the ladder a little bit higher. He was now one of the youngest Captains in the Army and in charge of 300 soldiers. He was about to return to the tent that passed for an office, when a private who looked about 19 ran up to him.

"Captain Muto, General Hall wants to speak to you! He's on a line communications tent."

Yugi sighed. Hall was the guy he was currently taking orders from. He would normally leave him and his men to their own devices, but when this freedom came with strings attached. When he called, it was invariably to give him a mission that was extreamly dangerous and that several other units had already failed at. "Alright, tell him I'll be there in three." The private nodded and ran off. Yugi, then ran to his personal tent, changed into a cleaner uniform and grabbed his cover. They weren't supposed to be worn indoors but having it with him would be a good sign. Making sure his pistol was properly in place, he made it to the communications tent with twelve seconds to spare. The inside was dimmly lit, with glowing computer and tv screens providing most of the light. At the back of the room, a gray haired man was shown on the largest screen. His uniform and smug look showed that he was in charge and he knew it.

"Hello, General. How can I help you today?" Yugi said with as much sarcasm as he could get away with.

"I have a little project for you, Captain Muto." His voice was dripping with supposed superiority and if he noticed the sarcasm, he didn't let on.

"And what might that be?" Yugi hated it when Hall talked down to him and his men.

Getting to buisness, the general said, "There is a dangerous new terrorist cell in your area who call themselves the War-mongers. The Pentagon believes that they are gathering the supplies neccessary for a nuclear bomb. I want you to hunt them down and end them before they can gain momentum."

"I'll get a team together imediately and send them out in a few days. This will be a top priority."

"Very good, but one more thing," something in Halls voice hade Yugi suspicious, but he hid it well. "I want you to personally lead the charge." That was certainly odd. He was the highest ranked officer in the camp. Why would Hall want him to leave?

"Yes, sir. We'll be ready within the week."

"Don't let me down," Hall said with almost cynical glee.

"I never do." Yugi said coldly.

* * *

There you go! What's going to happen next, and what is Hall's hidden agenda? Keep reading to find out.

For refrence, here are the main characters ages. Atem, 24. Yugi, 22. Joey, Tristan, Seto, Tea, all 22. Serenity, 19. Mokuba, 17.

P.S. I have decided to make it so that Domino City is in America. This is mainly due to the fact that I don't know anything about the Japanese military or customs and that kind of stuff. Being an American myself, it is much easier to write from this point of view. Just so you know because I never specified in the chapter. Also, the more reviews I get, the fast the next chapter will come.


	3. Rediscovery

I AM SOOOOOOO SORRY! I did not mean to take so long on this chapter. I just had a lot of stuff slowing me down. I promise the next one won't take nearly as long. Please read and review and don't hate me for my slowness. I really can't go anywhere without readers.

* * *

5 Days before Yugi's departure.

Seto Kaiba was in his office at Kaiba Corp looking over the flight plan in annoyance. He was going to India for a business conference, to prove to the board of directors that he was still involved in the business part of the company. Apparently they didn't think him personally making dozens of technological advances for the gaming community and hosting tournaments that promoted those advancements was enough. It really wasn't the fact that he was going that was annoying him, it was how he was getting there. Some idiot decided to send him straight over Afghanistan and the moment he figured out who, they were going to be fired. Didn't those idiots know there was a war going on there, never mind that there hadn't been any major fighting for a while, it was still legally a war zone! And what was worse, was that international flights had to be planned and filed weeks in advance. There was no time to change it now, and he couldn't back out or else he'd look like a coward. As he sat at his desk glaring at his computer screen, his little brother came in.

"What's got you so grumpy?," Mokuba asked.

"Take a look," Seto said in a monotone voice, turning the screen so Mokuba could see it clearly. The teenager raised his eyebrow upon seeing the flight path his brother was supposed to take. "Is that even legal?"

"It got approved so apparently."

"I don't like it. I just have a really bad feeling about this."

"I know, but you don't need to worry about me Mokuba. I can handle anything that comes my way."

"Alright, but you better swear that you'll make it back in one piece."

Seto laughed, now that his brother was older, the teenager was more aware than ever of the dangers they were both exposed to and as such, had become increasingly bossy about things like safety.

* * *

4 days before Yugi's departure.

Yugi looked around the tent at the people assembled there. His team was comprised of nine men, including himself and one woman. They were each the best in their area of expertise and were ready to face just about anything in the field. All of them were older than Yugi, if only be a few years in some cases, but they all sat and listened respectfully.

"Alright! Our first mission is purely recon. We know the Warmongers have a hideout somewhere in the region surrounding Jalalabad," Yugi said looking at the file in his hand and then pointing to the dot on a map behind him that indicated the city. "It's one of Afghanistan's largest cities and a major trading center. Plus being only about 50 miles from the border of Pakistan, it would be relatively easy to move supplies through. Now we are about twenty miles north of Kabul, which is about one-hundred miles west of Jalalabad. It will take one day to get there and then, the search begins. We will stay in the area for no more than five days, then return whether or not we have anything. We are unsure of this groups numbers, and need to proceed with caution. Remember while we are near the city, try to lay low and when you find enemy agents, observe only. Do not engage unless you absolutely have to. We need more information before we can launch an effective attack. Any questions?"

A man who looked to be about thirty and wore the markings of a second lieutenant raised his hand casually. "Yes, Lieutenant Brady?"

"What's the emergency protocol for this mission, Captain?"

Yugi kept his face blank, but was smiling on the inside. Brady was an expert on middle eastern languages, and could always be counted on to ask the important questions. "Alright, we'll set up a couple meeting points once we get there, but you need to know code words now, so you can get them memorized. We'll be using colors. Red, stands for injury. Blue, for identity compromise. Green, followed by your coordinates, means you need backup. Orange, means retreat to your designated meeting point and wait. Last, if I issue a code Black, it means to retreat to the meeting point, but one hour after it is issued to return to the camp with whoever has made it. I don't plan on using this, it's only as a last resort." They went over mission details for several more hours before leaving to complete what ever other business they had to do that day.

* * *

General Hall sat in a leather chair behind a rather large oak desk. He was looking at a computer, but the screen was positioned so it could not be seen by anyone else who might happen to come into the room.

"Well, does this arrangement satisfy you?," he asked the computer (which assumably had a connection to some unknown person) in a terse tone.

"Yes," said a voice that was obviously disguised. "It seems quite beneficial. I get a field officer who has been trusted with all the information my associates and I could possibly need, along with a few extra perks we can get from this particular individual. But what is it that you gain out of this?"

"I get to secure my position. The boy is advancing to fast for my liking. Muto is soon to be granted a ridiculous promotion. He will jump three ranks, from Captain to Colonel! It's unheard of, a twenty-two year old boy a Colonel. And what's worse, is that there are rumors going around that he is being looked at to take my place within the coming years. That is something I can not allow."

"If it is really that big of an issue, why do you not just stop the promotion. You are his commanding officer, are you not?"

"It is being issued by the President himself when Muto rotates back to the states. I could have him court martialed, but his record is flawless. Any inspection would prove his innocence within days. No, completely removing him from the equation is my only option. You will... dispose of him properly once you have what you need, correct?"

"Of course. That _is_ part of the deal. So long as he is _delivered_ as promised, the prodigy of a captain will die and no will ever know you were involved," mysterious voice said before they signed off.

"Perfect." The General then went about wiping his computer hard drive, so that no evidence of the conversation was left.

* * *

3 days before Yugi's departure.

It was Atem's first day at work since his return from Greece and he was quite happy to get back into his normal routine. His alarm had gone off at six o'clock. He got up, got ready and took the subway across town to the smaller Game Store that he ran. When he was about 100 yards from the door, he noticed a couple people who looked suspiciously like reporters standing there (almost certainly trying to find out about Yugi; they always were), and promptly made a b-line for the _back_ door of the building. At eight o'clock, the people were still there, but it was time to open so reluctantly Atem unlocked the door and changed the sign to open. He was drilled with questions as soon as they walked inside but dodged each one like a seasoned politician. After about thirty minutes, they realised they wouldn't get a story out of him and left. There were plenty of real customers that day too, but not many until after two o'clock. It was a school day after all, and most of his customers were students. He gave a few dueling lessons to a few of the regulars and had to deal with one man who decided to try and haggle over the price of an expensive card. The man didn't seem to understand the meaning of the words 'fixed price'. Despite the busyness, working in the store never ceased to refresh Atem, with the shear normalness of it all. It wasn't extravagant, like the life he had lived in Egypt, but he loved it. He loved not having to worry about the next attack or who was trying to steal the Millenium Items (Ishizu had them all locked up in a high security vault that only a few select people could access). He loved being able to know, more or less, what was going to happen to him each day. He only wished he had his brother here to share it with. That was all it would take, in his opinion, to make his life truly perfect. When evening came, Atem took the subway back home and ate dinner with his Grandpa, while they talked about their days. Then he went to bed, thinking that he would wake up and go through another ordinary day.

* * *

2 days before Yugi's departure.

Seto sat in the cabin of his private jet looking over the itinerary for the conference. It seemed to just be a week-long stream of meeting after meeting after presentation after meeting, with little time to rest in between. And most of them, he was only expected to be an observor. Well, that certainly wouldn't be the case. If he had to attend this stupid thing, the young CEO was planning to make sure everyone knew he was in charge, not sit quietly on the side-lines. It was his company after all. As he was reading the background information for one of the fist meetings, he was startled by the co-pilot yelling back to him. "Sir, we have a problem! You need to get yourself strapped in, NOW!" Seto did as he was told as he asked, "Why? What's going on?" "Missiles sir, heading our way! We're going to take evasive manuevers!" Then the plane turned so hard that it was flying sideways for a few seconds. During that time, Seto looked out the window and saw one of the missiles shot past, bearly missing one of the wings. Just as he was about to sign in relief, he heard a crash and a wave of heat come from behind him. He didn't have to look back. He knew that the rear of the aircraft had been hit and knew what was coming next, so he put his arms up against the seat in front of him and bent over to cover his head even before he heard the co-pilot yell at him to, "Brace yourself! We're going down! I see an airstrip ahead that we might be able to reach!"

Even though he wouldn't admit it later to anyone except Mokuba, in that moment he was terrified. Terrified that he might die. Terrified that he would never see his brother or his friends again. For a few moments, he really wasn't sure exactly how long, he lost all sense of his surrounding, then the impact came. The plane at first came down relatively level, but there was way to get purchase on the uneven ground of the Afghanistan desert. It was soon rolling on its side, the wings were torn off and at some point the cockpit and the cabin were separated. Seto had the sensation spinning as he was rolled over again and again inside what was left of his plane, until his head came into contact with something hard and his world began to go black just as the cabin came to a stop.

* * *

Yugi and the rest of his camp all watched in horror as the flaming aircraft hurtled toward the ground and towards them at a speed that even someone who knew nothing about planes would know was far to fast to be safe. He was trying to focus on it with a pair of binoculars, and when he finally got a clear image he gasped at the large, familiar KC logo. It was able to level out as it got closer to the ground and for a second, Yugi believed there would be a, if not nessecarilly safe, at least stable landing, but as the plane touched down nearly a mile away it was painfully clear that there was no purchase to be found on the rocky soil. Within seconds, the aircraft was rolling and being completely torn apart. Even before it stopped, Yugi was turning to his men and barking out orders. "That is an American Civilian aircraft! Get a medical team and fire squad out there now! Check for survivors and bring everyone back here immediately! GO!" He then turned back to look at the wreckage again. With the fire, he wasn't able to make out the tail number. But he had a feeling that he knew just who was on board. He just prayed he was wrong. However, he hid his worried well, as three trucks made their way out.

* * *

When Seto woke up, the first thing he noticed was the various tan colors that surrounded him. The close second was the throbbing pain that seemed to had taken over his whole body, especially his head. He closed his eyes and stayed still for a few minutes hoping that the pain would go down. It did slightly, but only just. When he heard the rustle of heavy fabric he opened his eyes again. A man had just walked into his... tent. He briefly wondered why he was in a tent, but turned his attention back to the man who had just entered. He was middle-aged with dark skin and black hair that was so short it was almost non-existent. He was also wearing a U.S. military uniform. He smiled when he was that Seto's eyes were open. "Good to see you're awake," he walked over and helped his sit up, which made Seto dizzy. Before he knew it, Seto was leaning over the edge of the cot he was on and emptying his stomach onto the floor. As he groaned the man put a small bucket under his chin. "Don't worry. Nausea is common with concutions and I think you have a pretty bad one. Now listen, my name is Doctor Williams and I need to ask you some questions." Seto nodded his consent.

"Alright first off, can you remember me your name?"

"Seto Kaiba."

"Good, next how old are you?"

"Twenty-two."

The questions were all just simple things about himself. It was a little annoying, but Seto knew what was going on, from a time he had a concussion when he was a kid. The doctor didn't need to find out who he was. No doubt they had already checked his I.D. and found whatever information they needed while he was knocked out. He had to make sure Seto didn't have any memory loss. When the questions were done, Dr. Williams shown a light into both of his eyes and his ears. He pressed a stethoscope to his chest and listened to his heartbeat. He briefly helped Seto stand up, but that only made him dizzier and so he sat back down quickly before he threw up again. When he was done giving Seto a basic check up he said, "Everything seems to check out. Just stay in bed for a few days and rest. I think that's all you really need. Oh, and this." He handed Seto a small orange pill bottle. "It's just a mild pain-killer. Take one in the morning, around noon and before you go to bed. Now the Captain wanted to talk to you when you woke up, but I'll only let him in if you feel up to it."

"I'm sure I can handle it," Seto deadpanned.

"Alright, I'll go get him," he left Seto alone in the large tent. A few minutes later, the tent flap opened again and someone else walked in. He was significantly shorter than the doctor who had treated him, and his fatigues, while nearly the same, held a different marking on the chest, collar and upper arms, signifying his higher rank. But Seto hardly noticed any of that. What first grabbed his attention were the four letters that spelled out his last name. Then he moved his gaze to look at the persons face in disbelief, wondering if he was hallucinating. His hair was short now and eyes had lost a lot of their child-like luster but there was no mistaking who this was.

"Yugi?! What the hell are you doing here?," Seto shouted at his friend.

"Well, I'm the Captain of this base," he said as if it were the most obvious thing in the world.

"Yeah, I can see that! But what the heck happened to you? How did you get in the Army!?"

"Sigh. Listen, I just wanted to come and see if you were alright. But it's late, and we both need some sleep. Rest, and I'll come back in the morning. I promise, I'll explain everything then."

"Fine, but you had better have some really good excuses for why you just up and disapeared," Seto was still mad, but he was also happy to see Yugi alive and so he gave him a small smirk.

"Ha, alright. I'll see you in the morning," he left with a small smile of his own. After that exchange Seto was sure he wouldn't get a wink of sleep, but knowing he needed it, he popped one of his pills in his mouth, rolled over on his cot and closed his eyes anyway.

* * *

There you go. The next one won't take nearly as long.


End file.
